Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

Aneuploidy and a deregulated DNA damage response suggest haploinsufficiency in breast tissues of BRCA2 mutation carriers

(2020) Mihriban Karaayvaz-Yildirim et al.   Science Advances

Heterotypic cell–cell communication regulates glandular stem cell multipotency

(2020) Alessia Centonze et al.   NATURE

Jointly defining cell types from multiple single-cell datasets using LIGER

(2020) Jialin Liu et al.   Nature Protocols

Rhabdomyosarcoma

(2019) Stephen X. Skapek et al.   Nature Reviews Disease Primers

Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment

(2019) Ana C. Garrido-Castro et al.   Cancer Discovery

Molecular Mechanisms of Polybrominated Diphenyl Ethers (BDE-47, BDE-100, and BDE-153) in Human Breast Cancer Cells and Patient-Derived Xenografts

(2019) Noriko Kanaya et al.   TOXICOLOGICAL SCIENCES

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Genomic signatures predict the immunogenicity of BRCA-deficient breast cancer

(2019) Adam A Kraya et al.   CLINICAL CANCER RESEARCH

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Latexin regulation by HMGB2 is required for hematopoietic stem cell maintenance

(2019) Cuiping Zhang et al.   HAEMATOLOGICA

Stathmin regulates the proliferation and odontoblastic/osteogenic differentiation of human dental pulp stem cells through Wnt/β-catenin signaling pathway

(2019) Xiaoyi Zhang et al.   Journal of Proteomics

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets

(2019) Frédéric Pont et al.   NUCLEIC ACIDS RESEARCH

Stem Cells and the Differentiation Hierarchy in Mammary Gland Development

(2019) Naiyang Fu et al.   PHYSIOLOGICAL REVIEWS

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

Stem Cells and Cellular Origins of Breast Cancer: Updates in the Rationale, Controversies, and Therapeutic Implications

(2019) Jiaojiao Zhou et al.   Frontiers in Oncology

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships

(2019) Chi-Yeh Chung et al.   Cell Reports

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Clinical Characteristics and Prognosis of Pregnancy-Associated Breast Cancer: Poor Survival of Luminal B Subtype

(2018) Soo Youn Bae et al.   ONCOLOGY

Dissecting the mammary gland one cell at a time

(2018) Simona Cristea et al.   Nature Communications

Emerging roles of Myc in stem cell biology and novel tumor therapies

(2018) Go J. Yoshida   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development

(2018) Rajshekhar R. Giraddi et al.   Cell Reports

Stathmin Is Required for Normal Mouse Mammary Gland Development and Δ16HER2-Driven Tumorigenesis

(2018) Ilenia Segatto et al.   CANCER RESEARCH

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Pregnancy duration and breast cancer risk

(2018) Anders Husby et al.   Nature Communications

Temporal Evaluation of Polybrominated Diphenyl Ether (PBDE) Serum Levels in Middle-Aged and Older California Women, 2011–2015

(2017) Susan Hurley et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The concentration-dependent effect of progesterone on follicle growth in the mouse ovary

(2017) Kouji KOMATSU et al.   JOURNAL OF REPRODUCTION AND DEVELOPMENT

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

(2017) Karsten Bach et al.   Nature Communications

Lineage-Restricted Mammary Stem Cells Sustain the Development, Homeostasis, and Regeneration of the Estrogen Receptor Positive Lineage

(2017) Alexandra Van Keymeulen et al.   Cell Reports

Lineage-Biased Stem Cells Maintain Estrogen-Receptor-Positive and -Negative Mouse Mammary Luminal Lineages

(2017) Chunhui Wang et al.   Cell Reports

Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level

(2017) Soheila Dolatabadi et al.   Frontiers in Genetics

Survivin: a unique target for tumor therapy

(2016) Himani Garg et al.   Cancer Cell International

SURVIVIN as a marker for quiescent-breast cancer stem cells—An intermediate, adherent, pre-requisite phase of breast cancer metastasis

(2016) Sumit Siddharth et al.   CLINICAL & EXPERIMENTAL METASTASIS

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Toward a Shared Vision for Cancer Genomic Data

(2016) Robert L. Grossman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection

(2016) Brian D. Lehmann et al.   PLoS One

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer

(2015) Deena M. A. Gendoo et al.   BIOINFORMATICS

ERrrr…Where are the Progenitors? Hormone Receptors and Mammary Cell Heterogeneity

(2015) Giusy Tornillo et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

The origin of breast tumor heterogeneity

(2015) A Skibinski et al.   ONCOGENE

MYC proteins promote neuronal differentiation by controlling the mode of progenitor cell division

(2014) N. Zinin et al.   EMBO REPORTS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Estrogen Plus Progestin and Breast Cancer Incidence and Mortality in the Women’s Health Initiative Observational Study

(2013) Rowan T. Chlebowski et al.   JNCI-Journal of the National Cancer Institute

Clinicopathological Features and Prognosis of Pregnancy Associated Breast Cancer – A Matched Case Control Study

(2013) Lilla Madaras et al.   PATHOLOGY & ONCOLOGY RESEARCH

Classifications within Molecular Subtypes Enables Identification of BRCA1/BRCA2 Mutation Carriers by RNA Tumor Profiling

(2013) Martin J. Larsen et al.   PLoS One

Progesterone pharmacokinetics in the mouse: implications for potential stroke therapy

(2012) Raymond Wong et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

Changing Concepts: Menopausal Hormone Therapy and Breast Cancer

(2012) R. T. Chlebowski et al.   JNCI-Journal of the National Cancer Institute

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

The biology of progesterone receptor in the normal mammary gland and in breast cancer

(2011) Alison E. Obr et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Defining the cellular precursors to human breast cancer

(2011) P. J. Keller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BRCA1 Basal-like Breast Cancers Originate from Luminal Epithelial Progenitors and Not from Basal Stem Cells

(2010) Gemma Molyneux et al.   Cell Stem Cell

Breast Cancer Subtypes and the Risk of Local and Regional Relapse

(2010) K. David Voduc et al.   JOURNAL OF CLINICAL ONCOLOGY

An assessment of sources and pathways of human exposure to polybrominated diphenyl ethers in the United States

(2009) Boris Johnson-Restrepo et al.   CHEMOSPHERE

Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers

(2009) Elgene Lim et al.   NATURE MEDICINE